7 sim output#9
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…tructures, and timing framework
…fying event calculations and configuration in SimConfig.
…ions and simulation output details
…x instead of neutrons_per_pulse for improved clarity and consistency
…per_pulse with particle_flux for improved clarity and consistency in timing model definitions.
…vent_spacing_ns and neutrons_per_pulse for improved clarity and consistency in timing configurations.
…_per_pulse with particle_flux for consistency in timing configurations.
…orking environment details
- Removed empty `__init__.py` files from `runner` and `sensor` directories. - Added documentation for the simulation working environment in `sim_environment.md`. - Introduced default simulation configuration payloads in `defaults.py`. - Created shared base models and primitive vectors for simulation config schemas in `base.py`. - Developed intensifier configuration models in `intensifier.py`. - Added metadata and run-environment models in `metadata.py`. - Implemented optical subsystem configuration models in `optical.py`. - Defined scintillator configuration models in `scintillator.py`. - Created sensor configuration models in `sensor.py`. - Developed primary source configuration models in `source.py`. - Introduced simulation and runner execution models in `simulation.py`.
…r, metadata, optics, scintillator, sensor, and source components
… RunEnvironmentIO
…s for consistency and improved module path handling
…ion for inline and file-backed optical curves
…py, timing.py - Deleted `io.py`, which contained HDF5 file and dataset access helpers. - Removed `plotting.py`, responsible for matplotlib rendering helpers. - Eliminated `secondaries.py`, which provided secondary-particle analysis helpers. - Deleted `spatial.py`, containing spatial quick-look plotting helpers. - Removed `timing.py`, which included timing analysis helpers for photon creation delays and decay fits.
…x, adjust pulse period and width, and set number of particles for Geant4 runner.
… per output configuration
… flushing based on event count
…simulation output path logic
…t in Geant4 runner
…rimaries, secondaries, and photons directories
…er output to 1000
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This pull request introduces significant improvements to the ScintiPix codebase, focusing on analysis module documentation, simulation documentation, and the addition of new skills and guidelines for working with agents, Python environments, and Pydantic models. The changes enhance clarity, maintainability, and usability for both developers and users.
Documentation and Guidelines
.agents/AGENTS.mdwith clear instructions for working with agents, emphasizing simplicity, and outlining the directory structure and module purposes..agents/docs/sim_environment.md), intensifier module (.agents/docs/intensifier.md), simulation outputs (.agents/docs/sim_output.md), and timing module (.agents/docs/timing.md). These documents describe configuration, output formats, and timing handling in detail. [1] [2] [3] [4] [5]Analysis Module Refactoring
analysis/README.mdto clarify the module's scope, layout, key entry points, and test instructions, making it easier for users to understand and use the analysis helpers.analysis/io.pyandanalysis/plotting.py, which contained shared HDF5 and matplotlib helper functions, likely in favor of new or refactored approaches. [1] [2]Skills and Best Practices
.agents/skills/pixi/SKILL.md, a thorough guide for managing Python environments with Pixi, including detection, dependency management, command execution, migration, and best practices..agents/skills/pydantic/SKILL.md, outlining best practices for creating and maintaining Pydantic models, with workflow steps and common pitfalls to avoid.These changes collectively improve developer onboarding, enforce best practices for environment and model management, and provide clear, user-friendly documentation for simulation and analysis workflows.